Microphthalmia, facial anomalies, microcephaly, thumb and hallux hypoplasia, and agammaglobulinemia

Cernunnos defect in an Iranian patient with T- B+ NK+ severe combined immunodeficiency: A case report and review of the literature

Background

Defective Cernunnos gene in nonhomologous end‐joining (NHEJ) pathway of the DNA repair is responsible for radiosensitive severe combined immunodeficiency (SCID). Herein, presented a new patient with Cernunnos deficiency and summarized the clinical, immunological, and molecular features of reported patients in the literature.

Case

The patient was a 6‐month‐old female born to consanguineous parents. She presented with long‐lasting fever, diarrhea, poor feeding, and restlessness. She had suffered from recurrent fever of unknown origin and multiple episodes of oral candidiasis. In the physical examination, microcephaly, failure to thrive, oral candidiasis, pustular rash on fingers, and perianal ulcers, but no dysmorphic feature were observed. The immunologic workup revealed lymphopenia, neutropenia, normocytic anemia, low T‐ but normal B‐ and natural killer (NK)‐ cells, low immunoglobulin (Ig)G, and normal IgA, IgM, and IgE. The T‐cell receptor excision circle (TREC) was low and the lymphocyte transformation test (LTT) was abnormal to mitogens and antigens. She was diagnosed with T⁻ B⁺ NK⁺ SCID and improved by intravenous immunoglobulin along with antimicrobials. A homozygous splice site variant, c.390 + 1G > T, at the intron 3 of the NHEJ1, was identified and the diagnosis of Cernunnos deficiency was established. However, while a candidate for hematopoietic stem cell transplantation, she developed sepsis and died at 11 months of age.

Conclusions

Cernunnos deficiency should be considered as a differential diagnosis in patients with microcephaly, growth retardation, recurrent infections, T‐cell defects, and hypogammaglobulinemia. The normal B‐cell level in the index patient is an unexpected finding in Cernunnos deficiency which requires further evaluation.

XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination

Repair of DNA double-strand breaks (DSBs) by the nonhomologous end-joining pathway (NHEJ) is important not only for repair of spontaneous breaks but also for breaks induced in developing lymphocytes during V(D)J (variable [V], diversity [D], and joining [J] genes) recombination of their antigen receptor loci to create a diverse repertoire. Mutations in the NHEJ factor XLF result in extreme sensitivity for ionizing radiation, microcephaly, and growth retardation comparable to mutations in LIG4 and XRCC4, which together form the NHEJ ligation complex. However, the effect on the immune system is variable (mild to severe immunodeficiency) and less prominent than that seen in deficiencies of NHEJ factors ARTEMIS and DNA-dependent protein kinase catalytic subunit, with defects in the hairpin opening step, which is crucial and unique for V(D)J recombination. Therefore, we aimed to study the role of XLF during V(D)J recombination. We obtained clinical data from 9 XLF-deficient patients and performed immune phenotyping and antigen receptor repertoire analysis of immunoglobulin (Ig) and T-cell receptor (TR) rearrangements, using next-generation sequencing in 6 patients. The results were compared with XRCC4 and LIG4 deficiency. Both Ig and TR rearrangements showed a significant decrease in the number of nontemplated (N) nucleotides inserted by terminal deoxynucleotidyl transferase, which resulted in a decrease of 2 to 3 amino acids in the CDR3. Such a reduction in the number of N-nucleotides has a great effect on the junctional diversity, and thereby on the total diversity of the Ig and TR repertoire. This shows that XLF has an important role during V(D)J recombination in creating diversity of the repertoire by stimulating N-nucleotide insertion.

A genomic copy number variant analysis implicates the MBD5 and HNRNPU genes in Chinese children with infantile spasms and expands the clinical spectrum of 2q23.1 deletion

Background

Infantile spasms (IS) is a specific type of epileptic encephalopathy associated with severe developmental disabilities. Genetic factors are strongly implicated in IS, however, the exact genetic defects remain unknown in the majority of cases. Rare mutations in a single gene or in copy number variants (CNVs) have been implicated in IS of children in Western countries. The objective of this study was to dissect the role of copy number variations in Chinese children with infantile spasms.

Methods

We used the Agilent Human Genome CGH microarray 180 K for genome-wide detection of CNVs. Real-time qPCR was used to validate the CNVs. We performed genomic and medical annotations for individual CNVs to determine the pathogenicity of CNVs related to IS.

Results

We report herein the first genome-wide CNV analysis in children with IS, detecting a total of 14 CNVs in a cohort of 47 Chinese children with IS. Four CNVs (4/47 = 8.5%) (1q21.1 gain; 1q44, 2q31.1, and 17p13 loss) are considered to be pathogenic. The CNV loss at 17p13.3 contains PAFAH1B1 (LIS1), a causative gene for lissencephaly. Although the CNVs at 1q21.1, 1q44, and 2q23.1 have been previously implicated in a wide spectrum of clinical features including autism spectrum disorders (ASD) and generalized seizure, our study is the first report identifying them in individuals with a primary diagnosis of IS. The CNV loss in the 1q44 region contains HNRNPU, a strong candidate gene recently suggested in IS by the whole exome sequencing of children with IS. The CNV loss at 2q23.1 includes MBD5, a methyl-DNA binding protein that is a causative gene of ASD and a candidate gene for epileptic encephalopathy. We also report a distinct clinical presentation of IS, microcephaly, intellectual disability, and absent hallux in a case with the 2q23.1 deletion.

Conclusion

Our findings strongly support the role of CNVs in infantile spasms and expand the clinical spectrum associate with 2q23.1 deletion. In particular, our study implicates the HNRNPU and MBD5 genes in Chinese children with IS. Our study also supports that the molecular mechanisms of infantile spasms appear conserved among different ethnic backgrounds.

Cernunnos influences human immunoglobulin class switch recombination and may be associated with B cell lymphomagenesis

B cells from Cernunnos-deficient patients contain aberrant class switch recombination junctions, and a dominant-negative Cernunnos mutation was detected in a diffuse large B cell lymphoma sample.

Cernunnos is involved in the nonhomologous end-joining (NHEJ) process during DNA double-strand break (DSB) repair. Here, we studied immunoglobulin (Ig) class switch recombination (CSR), a physiological process which relies on proper repair of the DSBs, in B cells from Cernunnos-deficient patients. The pattern of in vivo generated CSR junctions is altered in these cells, with unusually long microhomologies and a lack of direct end-joining. The CSR junctions from Cernunnos-deficient patients largely resemble those from patients lacking DNA ligase IV, Artemis, or ATM, suggesting that these factors are involved in the same end-joining pathway during CSR. By screening 269 mature B cell lymphoma biopsies, we also identified a somatic missense Cernunnos mutation in a diffuse large B cell lymphoma sample. This mutation has a dominant-negative effect on joining of a subset of DNA ends in an in vitro NHEJ assay. Translocations involving both Ig heavy chain loci and clonal-like, dynamic IgA switching activities were observed in this tumor. Collectively, our results suggest a link between defects in the Cernunnos-dependent NHEJ pathway and aberrant CSR or switch translocations during the development of B cell malignancies.

Genetics of hypogammaglobulinemia: what do we really know?

In the past, immunodeficiencies were categorized based on clinical and laboratory findings in the affected patient. Now we are more likely to define them based on the specific gene involved. One might expect this shift to increase the precision and clarity of diagnosis but in the last few years it has become increasingly clear that identification of a mutation in a specific gene may not tell the whole story. Some gene defects may reliably result in clinical disease, others may act as susceptibility factors that are more common in patients with immunodeficiency but can also be found in otherwise healthy individuals. Distinguishing between these two types of gene defects is essential for informative genetic counseling.

A newly recognized, likely autosomal recessive syndrome comprising agammaglobulinemia, microcephaly, craniosynostosis, severe dermatitis, and other features

We present a novel, likely autosomal recessive, multi-system disorder seen in three siblings, two males and one female, born to nonconsanguineous parents. The disease manifests as agammaglobulinemia with marked microcephaly, significant developmental delay, craniosynostosis, a severe dermatitis, cleft palate, narrowing of the choanae, and blepharophimosis. The constellation of clinical signs seen in this family likely represents a new and recognizable form of agammaglobulinemia due to a defect in early B-cell maturation.

Syndromic immunodeficiencies: genetic syndromes associated with immune abnormalities

In syndromic immunodeficiencies, clinical features not directly associated with the immune defect are prominent. Patients may present with either infectious complications or extra-immune medical issues. In addition to the immunologic abnormality, a wide range of organ systems may be affected. Patients may present with disturbances in skeletal, neurologic, dermatologic, or gastrointestinal function or development. These conditions can be caused by developmental abnormalities, chromosomal aberrations, metabolic disorders, or teratogens. For a number of these conditions, recent advances have resulted in an enhanced understanding of their genetic basis. The finding of immune deficits in a number of defined syndromes with congenital anomalies suggests that an underlying genetic syndrome should be considered in those patients in whom a significant non-immune feature is present.

Genes required for B cell development

Mutations in a variety of genes can cause congenital agammaglobulinemia and a failure of B cell development. The currently known genes encode components of the pre-B cell receptor or proteins that are activated by cross-linking of the pre-B cell receptor. Defects in these genes result in a block in B cell differentiation at the pro-B to pre-B cell transition. A patient with a translocation involving a previously unknown gene, LRRC8, demonstrated a block at exactly the same point in B cell differentiation (see the related article beginning on page 1707). It will be interesting to determine whether the protein encoded by this gene interacts with the pre-B cell receptor signal transduction pathway or is involved in a new pathway.

Early defects in B cell development

PURPOSE OF REVIEW

Recent clinical studies in patients with genetically proven X-linked or autosomal recessive agammaglobulinemia provide some guidelines that should influence our management of patients with suspected immunodeficiency.

RECENT FINDINGS

Males who are at a high risk of having X-linked agammaglobulinemia because they have an affected brother or uncle are often not evaluated for immunodeficiency until they are hospitalized for infection. Some of those who are evaluated are not started on gammaglobulin therapy immediately. More than 10% of patients with X-linked agammaglobulinemia are hospitalized for infection at less than 6 months of age, indicating that patients with known X-linked agammaglobulinemia should be started on therapy by 2-3 months of age. In patients with sporadic X-linked agammaglobulinemia, the incidence of chronic lung disease correlates with the age at diagnosis, highlighting the importance of early diagnosis. Although almost all patients who are diagnosed as having the condition at more than 12 months of age have a history of recurrent otitis, 93% are not evaluated for immunodeficiency until they are hospitalized for infection. Because the physical exam provides a clue to the diagnosis of the condition--unusually small or absent cervical lymph nodes and tonsils--it should be possible to make an early diagnosis in a greater percentage of patients. Patients with autosomal recessive agammaglobulinemia have an earlier onset of disease compared with patients with X-linked agammaglobulinemia and they are more likely to have severe complications of the disease.

SUMMARY

There is plenty of room for improvement in the diagnosis and management of patients with defects in early B cell development.